breseq  version 0.33.1  revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence seq id position mutation annotation gene description
RA CP000731 25,669 (A)7→6 coding (322/333 nt) USA300HOU_pUSA300HOUMR0031 → hypothetical protein
RA USA300TCH1516_ALE 39,378 C→A D586Y (GAT→TAT)  pbp ← Beta‑lactam‑inducible penicillin‑binding protein
RA USA300TCH1516_ALE 478,502 C→A D342E (GAC→GAA)  nuoL → NADH‑quinone oxidoreductase subunit L
RA USA300TCH1516_ALE 584,121 G→T intergenic (+205/‑67) rplA → / → rplJ 50S ribosomal protein L1/50S ribosomal protein L10
RA USA300TCH1516_ALE 707,909 A→T M1M (TTG→ATG) † znuC_1 ← High‑affinity zinc uptake system ATP‑binding protein ZnuC
RA USA300TCH1516_ALE 973,213 C→A E175* (GAG→TAG)  yitU_1 ← 5‑amino‑6‑(5‑phospho‑D‑ribitylamino)uracil phosphatase YitU
RA USA300TCH1516_ALE 1,002,200 T→G M173R (ATG→AGG)  mecA → Adapter protein MecA 1
RA USA300TCH1516_ALE 1,105,994 T→C T12T (ACT→ACC)  pdhD → Dihydrolipoyl dehydrogenase
RA USA300TCH1516_ALE 1,196,508 C→A S338Y (TCT→TAT)  ftsZ → Cell division protein FtsZ
RA USA300TCH1516_ALE 1,232,052 G→T D233Y (GAT→TAT)  stp → Serine/threonine phosphatase stp
RA USA300TCH1516_ALE 1,398,333 G→A Y101Y (TAC→TAT)  msrA1 ← Peptide methionine sulfoxide reductase MsrA 1
RA USA300TCH1516_ALE 1,416,458 A→T I216N (ATT→AAT)  oppD_4 ← Oligopeptide transport ATP‑binding protein OppD
RA USA300TCH1516_ALE 1,471,910 C→T E10038E (GAG→GAA)  ebh_1 ← Extracellular matrix‑binding protein ebh
RA USA300TCH1516_ALE 1,486,381 G→T Q5215K (CAA→AAA)  ebh_1 ← Extracellular matrix‑binding protein ebh
RA USA300TCH1516_ALE 1,513,930 A→T L413F (TTA→TTT)  USA300HOU_RS07375 → hypothetical protein
RA USA300TCH1516_ALE 1,539,250 C→G intergenic (‑349/+37) aroC ← / ← USA300HOU_RS07505 Chorismate synthase/hypothetical protein
RA USA300TCH1516_ALE 1,646,189 G→C A155G (GCA→GGA)  ypdF ← Aminopeptidase YpdF
RA USA300TCH1516_ALE 1,672,590 G→T L135I (CTT→ATT)  sigA ← RNA polymerase sigma factor SigA
RA USA300TCH1516_ALE 1,744,473 C→T A67T (GCT→ACT)  apt ← Adenine phosphoribosyltransferase
RA USA300TCH1516_ALE 2,010,363 C→T C146Y (TGT→TAT)  USA300HOU_RS10125 ← Putative multidrug export ATP‑binding/permease protein
RA USA300TCH1516_ALE 2,279,705 G→A A943V (GCA→GTA)  ebh_3 ← Extracellular matrix‑binding protein ebh
RA USA300TCH1516_ALE 2,289,324 G→T Q56K (CAG→AAG)  cdaA ← Cyclic di‑AMP synthase CdaA
RA USA300TCH1516_ALE 2,337,959 C→T intergenic (‑125/‑283) adhR ← / → USA300HOU_RS11940 HTH‑type transcriptional regulator AdhR/Hyaluronate lyase
RA USA300TCH1516_ALE 2,455,692 Δ1 bp coding (1210/1260 nt) lyrA → Lysostaphin resistance protein A
RA USA300TCH1516_ALE 2,455,698 2 bp→AT coding (1216‑1217/1260 nt) lyrA → Lysostaphin resistance protein A
RA USA300TCH1516_ALE 2,532,298 A→T T15T (ACA→ACT)  femA_3 → Aminoacyltransferase FemA
RA USA300TCH1516_ALE 2,679,803 G→T G96V (GGA→GTA)  ssaA2_4 → Staphylococcal secretory antigen ssaA2

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ CP000731 1 75 75 NA [0] [1] 2 –/repA –/replication protein A
* * ÷ CP000731 1613 1830 218 2 [1] [1] 2 repA/USA300HOU_pUSA300HOUMR0003 replication protein A/hypothetical protein
* * ÷ CP000731 3144 3207 64 2 [1] [1] 2 [USA300HOU_pUSA300HOUMR0005] [USA300HOU_pUSA300HOUMR0005]
* * ÷ CP000731 3762 4027 266 2 [1] [1] 2 [USA300HOU_pUSA300HOUMR0006] [USA300HOU_pUSA300HOUMR0006]
* * ÷ CP000731 6533 6584 52 2 [1] [1] 2 cadX/USA300HOU_pUSA300HOUMR0010 cadmium efflux regulator/MarR family transcriptional regulator
* * ÷ CP000731 7814 7910 97 2 [1] [1] 2 USA300HOU_pUSA300HOUMR0010/blaZ MarR family transcriptional regulator/beta‑lactamase
* * ÷ CP000731 9939 9999 61 3 [1] [1] 2 blaR beta‑lactamase regulator BlaR
* * ÷ CP000731 11612 11670 59 2 [1] [1] 2 USA300HOU_pUSA300HOUMR0014 recombinase
* * ÷ CP000731 12804–13239 13618 380–815 2 [1] [1] 2 [USA300HOU_pUSA300HOUMR0016] [USA300HOU_pUSA300HOUMR0016]
* * ÷ CP000731 14173 14435 263 2 [1] [1] 3 [USA300HOU_pUSA300HOUMR0018] [USA300HOU_pUSA300HOUMR0018]
* * ÷ CP000731 14815 14882 68 2 [1] [1] 2 USA300HOU_pUSA300HOUMR0018 3',5' aminoglycoside phosphotransferase
* * ÷ CP000731 15383 15463 81 2 [1] [1] 2 USA300HOU_pUSA300HOUMR0019 strepthothricin acetyltransferase
* * ÷ CP000731 15593 15637 45 2 [1] [0] 2 [USA300HOU_pUSA300HOUMR0019] [USA300HOU_pUSA300HOUMR0019]
* * ÷ CP000731 16324 16405–16402 79–82 2 [1] [1] 2 [USA300HOU_pUSA300HOUMR0021] [USA300HOU_pUSA300HOUMR0021]
* * ÷ CP000731 16494–16671 16671 1–178 2 [1] [1] 2 USA300HOU_pUSA300HOUMR0021 IS431 mec transposase
* * ÷ CP000731 17204 17310 107 2 [1] [1] 2 [USA300HOU_pUSA300HOUMR0023] [USA300HOU_pUSA300HOUMR0023]
* * ÷ CP000731 20011 20149 139 2 [1] [1] 2 USA300HOU_pUSA300HOUMR0024/USA300HOU_pUSA300HOUMR0027 bacitracin ABC ATP binding cassette transporter, ABC protein/IS431mec transposase
* * ÷ CP000731 21683 22202 520 3 [1] [1] 2 USA300HOU_pUSA300HOUMR0028 macrolide transporter
* * ÷ CP000731 22304 22451 148 2 [1] [1] 2 USA300HOU_pUSA300HOUMR0028 macrolide transporter
* * ÷ CP000731 23694 23798 105 2 [1] [1] 2 USA300HOU_pUSA300HOUMR0029 macrolide 2'‑phosphotransferase
* * ÷ CP000731 25149 25184 36 3 [1] [1] 2 USA300HOU_pUSA300HOUMR0030/USA300HOU_pUSA300HOUMR0031 Sin recombinase/hypothetical protein
* * ÷ CP000731 26933 27041 109 2 [1] [0] NA USA300HOU_pUSA300HOUMR0033/– partitioning protein/–

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? USA300TCH1516_ALE 512620 =148 (1.180)110 (1.250)
+40 bp		 67/190 0.1 51.4% intergenic (+688/‑6075) recR/speA_2 Recombination protein RecR/Arginine decarboxylase
?USA300TCH1516_ALE 1998278 = NA (NA)intergenic (‑6/+3329) USA300TCH1516_01882/USA300TCH1516_01883 tRNA‑Val/tRNA‑Ala